From b4917188b36704d5d9f37593523cad7923b26267 Mon Sep 17 00:00:00 2001
From: Thomas OBADIA <tobadia@pasteur.fr>
Date: Fri, 29 Apr 2022 16:28:03 +0200
Subject: [PATCH] Sanitize a possible error in subsetting colums for L (that
shouldn't have any consequences anyway) and harmonize grammar for
mutate(across()) statements
---
FUNCTIONS.R | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/FUNCTIONS.R b/FUNCTIONS.R
index aeb5cd6..e3bdc23 100644
--- a/FUNCTIONS.R
+++ b/FUNCTIONS.R
@@ -103,7 +103,7 @@ runRelativeAntibodyUnits = function(fname1, fname2, MFI_CSV, MFI_N_ANTIGENS, TEM
dim(L)
# MFI values as numeric
- L[,-which(colnames(L) %in% c("Location","Sample","Total Events","TotalEvents"))] = lapply(L[,-which(colnames(L) %in% c("Location","Sample","Total Events"))], as.numeric)
+ L[,-which(colnames(L) %in% c("Location","Sample","Total Events","TotalEvents"))] = lapply(L[,-which(colnames(L) %in% c("Location","Sample","Total Events","TotalEvents"))], as.numeric)
## Load the counts to check for run quality control
C = L_full[(count_row_number+1):(count_row_number+1+nrow(L)),1:(3+as.integer(MFI_N_ANTIGENS))]
@@ -177,7 +177,7 @@ runRelativeAntibodyUnits = function(fname1, fname2, MFI_CSV, MFI_N_ANTIGENS, TEM
L <- L %>% mutate_all(funs(gsub("NaN", 0, .)))
# MFI values as numeric
- L[,-which(colnames(L) %in% c("Location","Sample","Total Events","TotalEvents"))] = lapply(L[,-which(colnames(L) %in% c("Location","Sample","Total Events"))], as.numeric)
+ L[,-which(colnames(L) %in% c("Location","Sample","Total Events","TotalEvents"))] = lapply(L[,-which(colnames(L) %in% c("Location","Sample","Total Events","TotalEvents"))], as.numeric)
C <- as.data.frame(read_excel(fname1, skip = count_row_number+1, col_types = "text"))
@@ -247,7 +247,7 @@ runRelativeAntibodyUnits = function(fname1, fname2, MFI_CSV, MFI_N_ANTIGENS, TEM
C <- L %>%
dplyr::mutate(dplyr::across(!c(Location, Sample), gsub, pattern = "^(\\d+(?:\\.\\d+)?)(\\s*\\((\\d+(?:\\.\\d+)?)\\))?$", replacement = "\\3")) %>%
# Set to NA in case bead counts were not available
- dplyr::mutate(dplyr::across(!Location & !Sample, gsub, pattern = "^$", replacement = NA))
+ dplyr::mutate(dplyr::across(!c(Location, Sample), gsub, pattern = "^$", replacement = NA))
dim(C)
--
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